Woolly mammoths experienced a genomic meltdown just before extinction

March 2, 2017
Wooly mammoths near the Somme River, AMNH mural. Credit: Charles R. Knight, Public Domain, Wikimedia Commons

Dwindling populations created a "mutational meltdown" in the genomes of the last wooly mammoths, which had survived on an isolated island until a few thousand years ago. Rebekah Rogers and Montgomery Slatkin of the University of California, Berkeley, report these findings in a study published March 2nd, 2017 in PLOS Genetics.

Woolly mammoths were one of the most common large herbivores in North America, Siberia, and Beringia until a warming climate and human hunters led to their extinction on the mainland about 10,000 years ago. Small island populations persisted until about 3,700 years ago before the species finally disappeared. Researchers compared existing genomes from a mainland that dates back to 45,000 years ago, when the animal was plentiful, to one that lived about 4,300 years ago. The recent genome came from a mammoth that had lived in a group of about 300 animals on Wrangel Island in the Arctic Ocean. The analysis showed that the island mammoth had accumulated multiple harmful mutations in its genome, which interfered with gene functions. The animals had lost many olfactory receptors, which detect odors, as well as urinary proteins, which can impact social status and mate choice. The genome also revealed that the island mammoth had specific mutations that likely created an unusual translucent satin coat.

The comparison gives researchers the rare opportunity to see what happens to the genome as a population declines, and supports existing theories of genome deterioration stemming from small population sizes. The study also offers a warning to conservationists: preserving a small group of isolated animals is not sufficient to stop negative effects of inbreeding and genomic meltdown. For those interested in wooly mammoth "de-extinction," the study demonstrates that some mammoth genomes carry an overabundance of negative mutations.

Rebekah Rogers adds: "When I first started this project, I was excited to be working with the new woolly mammoth sequences, published by Love Dalen's lab. It was even more exciting when we found an excess of what looked like bad mutations in the mammoth from Wrangel Island. There is a long history of theoretical work about how genomes might change in small populations. Here we got a rare chance to look at snapshots of genomes 'before' and 'after' a population decline in a single species. The results we found were consistent with this theory that had been discussed for decades.

The mammoth analysis was also a great project to do with Monty Slatkin. He has spent his career developing mathematical models of how genomes will look different when population conditions change. With only two specimens to look at, these mathematical models were important to show that the differences between the two mammoths are too extreme to be explained by other factors."

Explore further: Woolly mammoth genomes offer insight into their history and extinction

More information: Rogers RL, Slatkin M (2017) Excess of genomic defects in a woolly mammoth on Wrangel island. PLoS Genet 13(3): e1006601. DOI: 10.1371/journal.pgen.1006601

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HannesAlfven
1 / 5 (5) Mar 02, 2017
Now, within this fresh context of mutations, should we once again ponder the recent finding of 7 examples of mammoth tusks peppered with small meteorite fragments?

http://www.nature...372.html

The same researchers also found a mammoth carcass partially covered in a black radioactive mat. See pictures here ...

The Extinction of the Mammoths
https://plus.goog...nTz57wfZ

The academic community wants us to believe that since these items date to 30-something thousand years, that the event can't have had anything to do with the far more recent extinction of the mammoths.

But, why again should these dates be accurate at all? The dating technique rests upon assumptions which such an event should violate.
jonesdave
4.5 / 5 (8) Mar 02, 2017
But, why again should these dates be accurate at all? The dating technique rests upon assumptions which such an event should violate.


And why wouldn't they be? Possibly because you want to tie it into some impossible Velikovskian nonsense, at a much later date? Get real.

HannesAlfven
1 / 5 (7) Mar 02, 2017
Settled science is science's great anti-pattern. The more rigorous approach would be to simply track the support which ALL ideas get over time, in order to erase the bias which historical ordering introduces into theory-making. When a former idea ACCIDENTALLY gains support, it actually should mean more than when people are actively cultivating evidence for their pet theory of the moment.

"Settled science" sometimes turns out to not be so settled after all, in the light of observations which reveal themselves, one-by-one, in a trickle, sometimes long after it became "settled". Since academics do not systematically track this situation, we have a fantastic opportunity here to disrupt modern science journalism.

A former Stanford Provost summed up the opportunity best just a couple of weeks ago ...
HannesAlfven
1 / 5 (7) Mar 02, 2017
http://news.stanf...-within/

The threat from within
February 21, 2017

Former Provost John Etchemendy, in a recent speech before the Stanford Board of Trustees, outlined challenges higher education is facing in the coming years. Following is an excerpt from that talk.

"Over the years, I have watched a growing intolerance at universities in this country – not intolerance along racial or ethnic or gender lines – there, we have made laudable progress. Rather, a kind of intellectual intolerance, a political one-sidedness, that is the antithesis of what universities should stand for. It manifests itself in many ways: in the intellectual monocultures that have taken over certain disciplines; in the demands to disinvite speakers and outlaw groups whose views we find offensive; in constant calls for the university itself to take political stands ..."
HannesAlfven
1 / 5 (7) Mar 02, 2017
(cont'd)

"We decry certain news outlets as echo chambers, while we fail to notice the echo chamber we've built around ourselves.

This results in a kind of intellectual blindness that will, in the long run, be more damaging to universities than cuts in federal funding or ill-conceived constraints on immigration. It will be more damaging because we won't even see it: We will write off those with opposing views as evil or ignorant or stupid, rather than as interlocutors worthy of consideration. We succumb to the all-purpose ad hominem because it is easier and more comforting than rational argument. But when we do, we abandon what is great about this institution we serve ..."

(cont'd)
HannesAlfven
1 / 5 (7) Mar 02, 2017
cont'd)

"It will not be easy to resist this current. As an institution, we are continually pressed by faculty and students to take political stands, and any failure to do so is perceived as a lack of courage. But at universities today, the easiest thing to do is to succumb to that pressure. What requires real courage is to resist it. Yet when those making the demands can only imagine ignorance and stupidity on the other side, any resistance will be similarly impugned.

The university is not a megaphone to amplify this or that political view, and when it does it violates a core mission. Universities must remain open forums for contentious debate, and they cannot do so while officially espousing one side of that debate ..."

(cont'd)
jonesdave
4.5 / 5 (8) Mar 02, 2017
Blah blah blah blah blah blah, ad infinitum. As per usual from Reeve. If you are talking about the moron Velikovsky, then you are basically saying to everyone reading: "I am an idiot. I don't understand science any better than he did. Feel free to take the **** out of me."
It is utter nonsense and has been debunked repeatedly over many decades. There is zero evidence for any of it. No scientist worth the name has ever taken it seriously. None ever will. It has nothing whatever to do with science, so why are you bringing it up on here, rather than some crank mythology woo site?
HannesAlfven
1 / 5 (7) Mar 02, 2017
(cont'd)

"But we must do more. We need to encourage real diversity of thought in the professoriate, and that will be even harder to achieve. It is hard for anyone to acknowledge high-quality work when that work is at odds, perhaps opposed, to one's own deeply held beliefs. But we all need worthy opponents to challenge us in our search for truth. It is absolutely essential to the quality of our enterprise.

I fear that the next few years will be difficult to navigate. We need to resist the external threats to our mission, but in this, we have many friends outside the university willing and able to help. But to stem or dial back our academic parochialism, we are pretty much on our own ..."

(cont'd)
HannesAlfven
1 / 5 (7) Mar 02, 2017
(cont'd)

"... The first step is to remind our students and colleagues that those who hold views contrary to one's own are rarely evil or stupid, and may know or understand things that we do not. It is only when we start with this assumption that rational discourse can begin, and that the winds of freedom can blow."
jonesdave
4.6 / 5 (9) Mar 02, 2017
^^^^^^^^^^^^^More irrelevant crap. Yawn. Nobody's listening Reeve, give it up. Go post it on dunderdolts or hollowscience.
HannesAlfven
1 / 5 (6) Mar 02, 2017
What is happening in academia today is a slow-motion handing over of the keys to the highest-order discourses in science from the established institutions to whoever will take the time to show up to accept them.

Academia is increasingly viewed as politicized by the public.

Science journalists as a rule only deliver the officially sanctioned worldview to academics who themselves are forced to specialize in ever thinner slices of the whole.

When the science journalists stopped reporting on controversial science in the 1910's and 20's, science itself became an organism which for the most part lacks cross-disciplinary systematic checks and balances.

Science has been cut up into fiefdoms, and the reporting leaves us with no indication of the vulnerability which this is creating.

We do not even know how many textbook theories are currently seriously challenged. We are likely talking hundreds of serious challenges by now with no reporting.
jonesdave
5 / 5 (7) Mar 02, 2017
^^^^^Finished? Right, I would suggest reading this paper:
The Younger Dryas impact hypothesis: A requiem.
Pinter, N. et al. (2011)
http://www2.nau.e.../135.pdf

In particular sections 2.1 & 2.2. It would appear that the meteorites aren't in fact meteorites. And the 'black mats' are nothing particularly unusual, either.
Captain Stumpy
4.3 / 5 (6) Mar 02, 2017
Now, within this fresh context of mutations, should we once again ponder the recent finding of 7 examples of mammoth tusks peppered with small meteorite fragments?
@chris reeve/hannes idiot
before you Gish-Gallop another ten irrelevant posts about bullsh*te, please tell us the direct reason why any mammoth tusk peppered with small meteorite fragments is relevant and to what you specifically are trying to promote by arguing that in every f*cking article that talks about mutation, mammoths or historical dating

more importantly, given that the above article actually references a study, then you must then show where your BELIEFS in your mammoth tusk argument:
a- is validated, thus supersedes the above study
b- proves the science in the study wrong
c- proves all the relevant referenced studies in the above study wrong

that is how the scientific method works

not by whinging in a pop-sci article seeking converts to a cult (eu)
but by presenting evidence
jonesdave
5 / 5 (6) Mar 02, 2017
@chris reeve/hannes idiot
before you Gish-Gallop another ten irrelevant posts about bullsh*te, please tell us the direct reason why any mammoth tusk peppered with small meteorite fragments is relevant and to what you specifically are trying to promote by arguing that in every f*cking article that talks about mutation, mammoths or historical dating


Oh, I can answer that. It'll all come down to Velikovskian woo. Reeve needs this stuff to happen a lot more recently. The fact that the dating is inconsistent means we must throw it away, because Velikovsky must be right. The total lack of evidence, such as ice core data to back up such woo, also means that has to be thrown out, in order that Venus can do handbrake turns around the solar system ca. 3000 years ago. All very simple :)

richdiggins
1 / 5 (3) Mar 02, 2017
The Younger Dryas impact hypothesis: A requiem.
Pinter, N. et al. (2011)
http://www2.nau.e.../135.pdf


That paper has a high level of hyperbole. I could write a better fable.

jonesdave
5 / 5 (5) Mar 02, 2017
The Younger Dryas impact hypothesis: A requiem.
Pinter, N. et al. (2011)
http://www2.nau.e.../135.pdf


That paper has a high level of hyperbole. I could write a better fable.



What the hell are you on about? Care to be specific? And no, I doubt you could, or ever have, written a scientific paper of any description.
Captain Stumpy
4 / 5 (4) Mar 02, 2017
The fact that the dating is inconsistent means we must throw it away, because Velikovsky must be right
@Jones
yeah, but the problem with reeves/hannes stupidity and Gish-Gallop BS argument is:
1- the dating method used in the study is based not only on evidence, but repeated studies that continue to make the dating methods more effective and accurate

2- science continues to validate the dating methods while also increasing it's accuracy

3- his stupid mammoth tusk link is singular, it does not have validation, nor does it in any way challenge the dating method or it's empirical evidence that has been repeatedly validated

so it's really stupid (and annoying) that the idiot continues to post this BS crap while not being able to actually produce evidence to refute the study and all the other validation studies

IOW- it's a cry-baby tantrum of "everyone must believe my pseudoscience because i can quote alfven out of context and everyone in science is a poopyhead"
richdiggins
1 / 5 (4) Mar 02, 2017
What the hell are you on about? Care to be specific? And no, I doubt you could, or ever have, written a scientific paper of any description.


Personally, I can do anything I put my mind to. That's why I am more successful than you.
Captain Stumpy
3.7 / 5 (3) Mar 02, 2017
Personally, I can do anything I put my mind to. That's why I am more successful than you.
Rule 37
Captain Stumpy
3.7 / 5 (3) Mar 03, 2017
Internet Rule 37 == "There are no girls on the internet....ever ."

so you're a /b/ro, then?
LMFAO

4-chan party van making stops at all locations near you!
LOL

(see also v&)

OOPS

PS
rule 37 can also reference "failure to disclose" or present evidence - though i particularly like the 4chan quote as it's succinct and accurate: there are no [insert claim here] on the net... ever
jonesdave
5 / 5 (4) Mar 03, 2017
What the hell are you on about? Care to be specific? And no, I doubt you could, or ever have, written a scientific paper of any description.


Personally, I can do anything I put my mind to. That's why I am more successful than you.


Err, no, you're not, as you are obviously at least as scientifically illiterate as Reeve. What you meant to say was: "I am too stupid to actually understand the paper, and don't care, as I want to carry on believing in fairy stories."
richdiggins
1 / 5 (2) Mar 03, 2017
PS
rule 37 can also reference "failure to disclose" or present evidence - though i particularly like the 4chan quote as it's succinct and accurate: there are no [insert claim here] on the net... ever


No proof is necessary on this forum. Ad hominem rules the day.

As far as the jonesdave fellow, as anyone can tell from his tenuous use of the english language, that he is both confrontational and feeble minded. Just those two traits alone can be a serious handicap in today's society. Just an observation.

Personally, I am not here to have playground arguments.
jonesdave
5 / 5 (1) Mar 03, 2017
Personally, I am not here to have playground arguments.


Hey, idiot, did I not ask you to expand on your original post? Discuss the science. You're the one going off on a gish gallop due to not being scientifically literate enough to understand the paper you criticised. Moron.
richdiggins
1 / 5 (3) Mar 03, 2017
Instead, I will invoke the old aphorism "if it ain't broke, don't fix it."
jonesdave
5 / 5 (1) Mar 03, 2017
Instead, I will invoke the old aphorism "if it ain't broke, don't fix it."


If what isn't broke?????? You really are a nutjob, aren't you? The latter is a rhetorical question, by the way.
Just admit that you are incapable of understanding the paper, and then we can all move on, rather than you doing anything to avoid addressing the question.
richdiggins
1 / 5 (3) Mar 03, 2017

If what isn't broke?????? You really are a nutjob, aren't you? The latter is a rhetorical question, by the way.
Just admit that you are incapable of understanding the paper, and then we can all move on, rather than you doing anything to avoid addressing the question.


You're broken, son.
I am pointing out its not my job to correct your behavior and/or that paper you linked to.

You are far too confrontational... as such it would be foolish to continue trying to have a conversation with someone such as yourself.
jonesdave
5 / 5 (3) Mar 03, 2017

If what isn't broke?????? You really are a nutjob, aren't you? The latter is a rhetorical question, by the way.
Just admit that you are incapable of understanding the paper, and then we can all move on, rather than you doing anything to avoid addressing the question.


You're broken, son.
I am pointing out its not my job to correct your behavior and/or that paper you linked to.

You are far too confrontational... as such it would be foolish to continue trying to have a conversation with someone such as yourself.


Translation: "I don't understand the paper, and was a pillock for making my initial comment. Now I'm going to run away, having contributed zero scientific comments to the thread."

Typical EU woo merchant behaviour. Some things never change. Your name's not Wal, is it?
434a
5 / 5 (5) Mar 03, 2017
Settled science is science's great anti-pattern....etc


To summarise; no-one's listening to me and it's not fair. Scientists are all close minded meanies who won't let me play with them.

The bizarre thing is anyone is welcome to play, science is one of the most inclusive of all activities, all you have to do is follow the rules. And the rules aren't there to exclude you, they are there so that everyone else can follow along and have a common frame of reference to understand when a point has been scored.

What you seem to want is for people to relax the rules so you can join in. Actually relax is a bit in accurate, throw away is more like it. We've all turned up to the stadium to play Humanity vs The Unknown and you're in the car park complaining no-one is letting you in when the gate is clearly open and the tickets are free. All we are asking is you play with leather ball and not the cucumber you've bought along.


Captain Stumpy
3.7 / 5 (3) Mar 03, 2017
No proof is necessary on this forum. Ad hominem rules the day
@richdiggins
if you want to talk science then proof must be a part of the argument (proof as in evidence, or the validation of your claims)
therefore the former is absolutely wrong

the latter argument about ad hominem is only correct because the failure of the site to actually abide by it's guidelines
their failure leaves the same small group of verbose sock using cult acolytes posting the same pseudoscience or stupidity, and as such, they somehow think that repetition is equivalent to fact

example:
cantdrive is decimated by a factual physics argument here: https://phys.org/...ggs.html

yet you can see all those same arguments proven false in that one thread repeated ad nauseum since, while still never once actually producing source material from a reputable journal

that is why ad hominem rules on PO
TheGhostofOtto1923
4 / 5 (4) Mar 03, 2017
"The analysis showed that the island mammoth had accumulated multiple harmful mutations in its genome, which interfered with gene functions."

-Wonder if the same evidence can be found in the typical domesticated human? Or civilized vs hunter-gatherer? Do conditions like morbid obesity and autism result from the absence of natural selection?

And how does war affect the relative fitness of populations? Were euros in general healthier and more sane after the world wars than before?
Chris_Reeve
1 / 5 (2) Mar 04, 2017
Re: "Settled science is science's great anti-pattern....etc ... Re: To summarise; no-one's listening to me and it's not fair. Scientists are all close minded meanies who won't let me play with them."

No.

At each historical moment, history provides a worldview through which we view the world.

What I'm saying is that history makes a mockery of the idea of settled science.

To suggest that we can call matters settled is to say that there is no history which affects our worldview.

But, the truth is that we have no choice but to look at future revelations from the lens of past knowledge.

History itself creates a bias.

To get past it, you have to track all claims.

It doesn't matter that many claims will prove to be wrong.

The very existence of history means that all of our observations are biased.

The only way past that is to track all claims over time.

Anything less is honestly lazy.
Chris_Reeve
1 / 5 (3) Mar 04, 2017
Think about it this way.

There used to be a lively debate over the mammoths and their extinction.

It is today assumed that they were slaughtered by humans and/or climate change.

That question is treated as settled science.

Yet, since then, we've found 7 mammoth tusks that have meteorites embedded in them, on one side.

A mammoth carcass was found that was partially draped by a black radioactive mat with exotic isotopes.

The tusks dated to tens of thousands of years, but there are violations here of the assumptions necessary for accurate dating. There's no reason why these dates should be accurate.

Researchers are ignoring these observations ...

Never forget that the proxies rely upon many assumptions.
SlartiBartfast
3.7 / 5 (3) Mar 04, 2017

That question is treated as settled science.


No, any new evidence is open to consideration.


Yet, since then, we've found 7 mammoth tusks that have meteorites embedded in them, on one side.


So? That's not even remotely inconsistent with current ideas of mammoth extinction.


A mammoth carcass was found that was partially draped by a black radioactive mat with exotic isotopes.


Funny that the only things that come up when I google "wooly mammoth radioactive mat" are you making this strange claim. Not only does there seem to be no evidence for it, but it's unclear how it's even relevant to anything.


The tusks dated to tens of thousands of years, but there are violations here of the assumptions necessary for accurate dating. There's no reason why these dates should be accurate.


So sayeth the creationists.


Researchers are ignoring these observations ...


It's a conspiracehhhh!
Captain Stumpy
3 / 5 (2) Mar 05, 2017
@hannes/reeve eu pseudoscience cultist
Yet, since then, we've found 7 mammoth tusks that have meteorites embedded in them, on one side
so you can't actually provide evidence, therefore you Gish-Gallop again?

1- so what about the tusks?

2- using your exact same logic, we can also state that because there were mammoth tusks with meteorites in them then calendars don't have weeks

IOW - you show no correlation, cause, evidence, links, or even a rational argument as to why you think your tusks beliefs are even relevant to the topic, let alone are proof of anything regarding the mammoths study above

given that the above article actually references a study, then you must then show where your beliefs in your mammoth tusk argument: (all apply)
a- is validated, thus supersedes the above study

b- proves the science in the study wrong

c- proves all the relevant referenced studies in the above study wrong

434a
5 / 5 (2) Mar 06, 2017

No.

At each historical moment, history provides a worldview through which we view the world.



I've never heard a scientist use the term settled science, it's not even a concept any scientist would be comfortable with.
That term seems to be of your own creation and it would also seem that it is the foundation of sand you have built your intellectual house upon.

The most famous transition I can think of was Newtonian Mechanics to GR and SR.
In less than a decade Einstein changed the face of Physics by presenting a mathematical model that was testable against the observable universe.
I didn't hear that he claimed there was settled science or that there was some sort of stitch-up or bias that would prevent him from publishing.
He had an idea, wrote the papers, put them into the public domain for criticism and had them accepted based on their performance against observations.
Cont..
434a
5 / 5 (1) Mar 06, 2017
I cannot think of a more daunting challenge than to face-off against Newton and his 200 plus year old legacy.
If you have something that could overturn GR/SR then publish it, move humanity forward.
Einstein's legacy is only 100 years old, a mere twinkle in a physicist's eye.

Having had a chance to read your other posts on here I wonder why you feel you need to defend your faith in this way?
Faith doesn't require mathematical models, faith, by its very definition, does not want or require proof.
Proof removes the need for faith, is that your intention?
Anyone who actually has faith does not feel in the least bit threatened by science.

If you can't bring yourself to accept that the creation story is just that, why not choose to believe the universe was created old.
At least that way you don't need to contrive a flawed model of the universe, it does nothing but undermine true faith.

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